Pakistan's president says in a newspaper interview, he harbored long-time suspicions that something was amiss in his country's nuclear weapons program, but delayed acting on the matter because he lacked proof. Pakistan's top nuclear scientist, Abdul Qadeer Khan, has confessed to selling nuclear secrets abroad, and was subsequently pardoned by the president, General Pervez Musharraf. Questions persist over who else was involved in the illicit nuclear trade.

For at least 15 years, and perhaps longer, Mr. Khan was able to run what some are calling a nuclear arms bazaar as a side business to his regular job running Pakistan's top nuclear research facility. He enriched himself by selling his country's nuclear secrets to Iran, Libya and North Korea and, analysts say, perhaps other countries, as well.

Mr. Khan was finally caught in large part due to evidence from British and U.S. intelligence agencies. But, instead of being prosecuted as a traitor, Mr. Khan was hailed as a national hero. In a series of choreographed steps, Mr. Khan went on state-run TV to confess, and was pardoned by General Musharraf the following day.

Husain Haqqani was an advisor to three prime ministers and is currently a visiting scholar at the Carnegie Endowment for International Peace. He says the confession and the pardon are part of a cover-up to hide the involvement of important people.

"It is essentially a deal to try and ensure that the full details of what actually happened and whoever sanctioned it and whoever was involved is revealed - if at all - only privately to U.S. intelligence, and not necessarily in the public domain," he said.

Mr. Khan insists he was acting on his own, without any assistance or authority from higher up. But that claim sparks skepticism from many who question how such a nuclear marketplace could have operated under the eyes of Pakistani security.

General Musharraf has said he knew nothing of the nuclear market. In an interview in The New York Times newspaper Tuesday, the Pakistani president says he suspected Mr. Khan of the illicit activity for about three years. But he says that it was not until October that U.S. officials gave him enough evidence to strip Mr. Khan of his post as a special government advisor.

Mr. Haqqani believes there had to be heavy military involvement in the nuclear market, including, perhaps, that of General Musharraf himself. "Well, it would be highly unlikely, when the previous military chief handed over to General Pervez Musharraf he did not tell him everything that he and the military were doing at the time," he said. "So, if the previous military chiefs knew, then General Pervez Musharraf knew."

Others disagree. Brian Cloughley is a former Australian military attache in Islamabad, and author of a well-respected book on the Pakistani army. Mr. Cloughley, who met with General Musharraf as recently as last month, says that, while there was probably some military participation, he believes it very unlikely that General Musharraf was involved.

"I think it's unlikely, however, that he would have been, for the simple reason that he is very, very jealous of Pakistan's security, perhaps verging on the, well, I wouldn't want to say the paranoid, but extremely concerned about any sort of information that would leave Pakistan on the nuclear side," he said.

The country's previous civilian leaders, former prime ministers Benazir Bhutto and Nawaz Sharif, have said the military kept them in the dark about much of the super-secret nuclear weapons program. However, says Mr. Cloughley, he does not buy the story that the prior civilian governments were as ignorant as they claim.

"Oh, if there was money involved, I would say they were probably to the fore in this," he said. "They knew everything about the nuclear program. They weren't that much in the dark. It's conventional wisdom now, of course, spread by the two disenchanted former leaders, that they were kept out of everything. They may have been venal. They may have been corrupt. But I don't think they were that stupid. There can be no doubt that, if there was something going on on the scale that it was until, I believe, comparatively recently - perhaps about 2000 - then they must have known."

Although Mr. Khan was pardoned, six of his close aides are also implicated. However, it is not clear if they will ever face trial because of the sensitive issues they might raise.